BitSeq

DOI: 10.18129/B9.bioc.BitSeq    

Transcript expression inference and differential expression analysis for RNA-seq data

Bioconductor version: Release (3.7)

The BitSeq package is targeted for transcript expression analysis and differential expression analysis of RNA-seq data in two stage process. In the first stage it uses Bayesian inference methodology to infer expression of individual transcripts from individual RNA-seq experiments. The second stage of BitSeq embraces the differential expression analysis of transcript expression. Providing expression estimates from replicates of multiple conditions, Log-Normal model of the estimates is used for inferring the condition mean transcript expression and ranking the transcripts based on the likelihood of differential expression.

Author: Peter Glaus, Antti Honkela and Magnus Rattray

Maintainer: Antti Honkela <antti.honkela at hiit.fi>, Panagiotis Papastamoulis <panagiotis.papastamoulis at manchester.ac.uk>

Citation (from within R, enter citation("BitSeq")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("BitSeq")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BitSeq")

 

PDF R Script BitSeq User Guide
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews AlternativeSplicing, Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Sequencing, Software, Transcription
Version 1.24.0
In Bioconductor since BioC 2.10 (R-2.15) (6.5 years)
License Artistic-2.0 + file LICENSE
Depends Rsamtools, zlibbioc
Imports S4Vectors, IRanges
LinkingTo Rsamtools(>= 1.19.38), zlibbioc
Suggests edgeR, DESeq, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BitSeq_1.24.0.tar.gz
Windows Binary BitSeq_1.24.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) BitSeq_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BitSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BitSeq
Package Short Url http://bioconductor.org/packages/BitSeq/
Package Downloads Report Download Stats

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